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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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) 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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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) 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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $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' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ), 'gf_id' => 'HOM05D001578', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001578' ), 'data_identifier' => 'HOM05D001578', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001578', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '406', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37160' => 'bna', 'A01p37170' => 'bna', 'A03p40090' => 'bna', 'A05p32610' => 'bna', 'A06p04790' => 'bna', 'Aa31LG10G5830' => 'aar', 'Aa31LG8G4140' => 'aar', 'Actinidia13347' => 'ach', 'Actinidia18465' => 'ach', 'Actinidia18466' => 'ach', 'Actinidia21379' => 'ach', 'Ah.08g216390' => 'amhyb', 'Ah.08g216400' => 'amhyb', 'AL1G54460' => 'aly', 'AL3G30110' => 'aly', 'AL3G30120' => 'aly', 'Aqoxy2G02876' => 'aox', 'Aqoxy2G03024' => 'aox', 'arahy.Tifrunner.gnm1.ann1.HZ07NS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5N9NX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T9CDYU' => 'arhy', 'AT1G47960' => 'ath', 'AT3G17130' => 'ath', 'AT3G17140' => 'ath', 'Atru.chr4.3054' => 'acertr', 'Atru.chr4.3056' => 'acertr', 'Atru.chr4.3057' => 'acertr', 'AUR62009839' => 'cqu', 'AUR62038151' => 'cqu', 'BcaB04g18931' => 'bca', 'BcaB04g18932' => 'bca', 'BcaB04g20862' => 'bca', 'BcaB04g20863' => 'bca', 'BcaB06g25805' => 'bca', 'BcaB07g33804' => 'bca', 'BcaC01g03784' => 'bca', 'BcaC01g03785' => 'bca', 'BcaC05g28823' => 'bca', 'BcaC08g42990' => 'bca', 'BcaC09g48669' => 'bca', 'BcaC09g48670' => 'bca', 'BolC1t04676H' => 'bol', 'BolC1t04679H' => 'bol', 'BolC3t17144H' => 'bol', 'BolC3t17145H' => 'bol', 'BolC5t33672H' => 'bol', 'BolC6t35358H' => 'bol', 'BraA01t03777Z' => 'bra', 'BraA01t03778Z' => 'bra', 'BraA03t13159Z' => 'bra', 'BraA03t13160Z' => 'bra', 'BraA05t22085Z' => 'bra', 'BraA06t23683Z' => 'bra', 'C01p47100' => 'bna', 'C01p47110' => 'bna', 'C03p48660' => 'bna', 'C03p48670' => 'bna', 'C05p49310' => 'bna', 'C06p02320' => 'bna', 'CAN.G1075.28' => 'can', 'CAN.G13.19' => 'can', 'CAN.G1359.1' => 'can', 'CAN.G1692.2' => 'can', 'CAN.G1913.1' => 'can', 'CAN.G1971.3' => 'can', 'CAN.G305.59' => 'can', 'CAN.G484.68' => 'can', 'CAN.G484.69' => 'can', 'CAN.G913.13' => 'can', 'CANSAT78G0727' => 'cansat', 'CANSAT78G2386' => 'cansat', 'CARHR037570' => 'chi', 'CARHR037580' => 'chi', 'CARHR088530' => 'chi', 'CARHR088540' => 'chi', 'CARHR092380' => 'chi', 'CARHR092390' => 'chi', 'CARHR268400' => 'chi', 'Carub.0001s3704' => 'cru', 'Carub.0003s1687' => 'cru', 'Carub.0003s1688' => 'cru', 'Ca_00963_v3' => 'car', 'Ca_21409_v3' => 'car', 'Ca_21410_v3' => 'car', 'Ca_21411_v3' => 'car', 'Ca_21424_v3' => 'car', 'Ca_21425_v3' => 'car', 'Cc03_g00590' => 'ccan', 'Cc03_g00600' => 'ccan', 'Cfa006332' => 'cfa', 'Cfa015283' => 'cfa', 'Cfa015284' => 'cfa', 'Cfa020792' => 'cfa', 'Ciclev10002621m.g' => 'ccl', 'Ciclev10003542m.g' => 'ccl', 'Ciclev10004017m.g' => 'ccl', 'Ciclev10006032m.g' => 'ccl', 'Ciclev10006511m.g' => 'ccl', 'Ciclev10006791m.g' => 'ccl', 'Ciclev10013964m.g' => 'ccl', 'CiPaw.01G135600' => 'cil', 'CiPaw.01G135800' => 'cil', 'CiPaw.01G135900' => 'cil', 'CiPaw.01G136000' => 'cil', 'COL.COLO4_34577' => 'col', 'COL.COLO4_34578' => 'col', 'COL.COLO4_34581' => 'col', 'Cpa.g.sc9.24' => 'cpa', 'Cpa.g.sc9.25' => 'cpa', 'Cpa.g.sc9.27' => 'cpa', 'CSS0012414' => 'camsi', 'CSS0020686' => 'camsi', 'CSS0037733' => 'camsi', 'CSS0047439' => 'camsi', 'DCAR_023358' => 'dca', 'Dinv44262' => 'din', 'Duzib052G0195' => 'dzi', 'Duzib052G0880' => 'dzi', 'Duzib052G1048' => 'dzi', 'Duzib151G0004' => 'dzi', 'Duzib151G0695' => 'dzi', 'Duzib151G1057' => 'dzi', 'Duzib177G0524' => 'dzi', 'ECA233G4032' => 'eca', 'ECA233G5780' => 'eca', 'EL10Ac7g16354' => 'bvu', 'EL10Ac7g16355' => 'bvu', 'Eucgr.B03967' => 'egr', 'Eucgr.B03968' => 'egr', 'Eucgr.H04067' => 'egr', 'Eucgr.H04068' => 'egr', 'Eucgr.H04069' => 'egr', 'Eucgr.L02838' => 'egr', 'Eucgr.L02839' => 'egr', 'Eucgr.L02840' => 'egr', 'FAN02G2223' => 'fan', 'FAN07G0539' => 'fan', 'FAN07G0948' => 'fan', 'FAN07G1428' => 'fan', 'FAN07G2152' => 'fan', 'FAN07G2406' => 'fan', 'FAN07G2927' => 'fan', 'FAN12G0910' => 'fan', 'FAN12G2012' => 'fan', 'FAN12G2021' => 'fan', 'FAN12G2195' => 'fan', 'FAN17G3073' => 'fan', 'FAN18G0021' => 'fan', 'FAN22G0905' => 'fan', 'FAN22G2269' => 'fan', 'FvH4_1g05890' => 'fve', 'FvH4_4g14140' => 'fve', 'FvH4_4g20180' => 'fve', 'FvH4_4g20430' => 'fve', 'FvH4_4g20440' => 'fve', 'FvH4_4g20480' => 'fve', 'FvH4_4g20510' => 'fve', 'FvH4_4g25190' => 'fve', 'FvH4_4g25210' => 'fve', 'FvH4_5g04330' => 'fve', 'FvH4_5g19730' => 'fve', 'FvH4_6g33790' => 'fve', 'Glyma.07G237300' => 'gma', 'Glyma.07G237500' => 'gma', 'Glyma.09G033700' => 'gma', 'Glyma.15G138400' => 'gma', 'Glyma.17G036100' => 'gma', 'Glyma.17G036300' => 'gma', 'Glyma.17G036400' => 'gma', 'Glyma.20G028700' => 'gma', 'Glyma.20G028900' => 'gma', 'Glyma.20G029000' => 'gma', 'Glyma.20G029200' => 'gma', 'Glyma.20G029500' => 'gma', 'Glyma.20G029700' => 'gma', 'Gohir.A01G035200' => 'ghi', 'Gohir.A01G035300' => 'ghi', 'Gohir.A05G275500' => 'ghi', 'Gohir.A10G174050' => 'ghi', 'Gohir.A10G174100' => 'ghi', 'Gohir.D01G023565' => 'ghi', 'Gohir.D01G023568' => 'ghi', 'Gohir.D05G277600' => 'ghi', 'Gohir.D10G180600' => 'ghi', 'Gohir.D10G180700' => 'ghi', 'Gorai.002G031100' => 'gra', 'Gorai.002G031200' => 'gra', 'Gorai.009G290600' => 'gra', 'Gorai.011G202100' => 'gra', 'Gorai.011G202200' => 'gra', 'HanXRQChr13g0393461' => 'han', 'HanXRQChr13g0395151' => 'han', 'HanXRQChr13g0395161' => 'han', 'HanXRQChr13g0395171' => 'han', 'HanXRQChr13g0395201' => 'han', 'HanXRQChr13g0395211' => 'han', 'HanXRQChr13g0395221' => 'han', 'Haze_01333' => 'cav', 'Haze_01334' => 'cav', 'Haze_01338' => 'cav', 'Haze_01339' => 'cav', 'Haze_04447' => 'cav', 'Haze_04455' => 'cav', 'Hma1.2p1_0078F.1_g039850' => 'hma', 'Hma1.2p1_1400F.1_g280915' => 'hma', 'Lalb_Chr07g0181921' => 'lal', 'Lalb_Chr07g0181931' => 'lal', 'Lalb_Chr07g0181941' => 'lal', 'Lalb_Chr07g0181951' => 'lal', 'Lalb_Chr09g0332371' => 'lal', 'Lalb_Chr11g0072061' => 'lal', 'Lalb_Chr12g0200771' => 'lal', 'Lalb_Chr12g0200781' => 'lal', 'Lalb_Chr12g0200791' => 'lal', 'Lalb_Chr13g0298611' => 'lal', 'Lalb_Chr13g0298621' => 'lal', 'Lalb_Chr13g0298631' => 'lal', 'Lalb_Chr13g0298651' => 'lal', 'Lalb_Chr13g0298661' => 'lal', 'Lalb_Chr15g0089101' => 'lal', 'Lalb_Chr20g0117771' => 'lal', 'Lalb_Chr22g0352521' => 'lal', 'Lj1g0016642' => 'lja', 'Lj1g0019408' => 'lja', 'Lj3P834T42' => 'lonja', 'Lj3P834T43' => 'lonja', 'Lj4g0009388' => 'lja', 'Lj4g0019348' => 'lja', 'Lj4g0021583' => 'lja', 'Lj6g0003953' => 'lja', 'Lj6g0013229' => 'lja', 'Lsat_1_v5_gn_5_185380' => 'lsa', 'Lsat_1_v5_gn_5_185420' => 'lsa', 'Lsat_1_v5_gn_6_301' => 'lsa', 'Lsat_1_v5_gn_7_59300' => 'lsa', 'Lsat_1_v5_gn_7_59360' => 'lsa', 'Lsat_1_v5_gn_7_59420' => 'lsa', 'Manes.02G201700' => 'mes', 'Manes.03G207000' => 'mes', 'Manes.03G207100' => 'mes', 'Manes.15G002000' => 'mes', 'Manes.15G002100' => 'mes', 'Manes.15G098100' => 'mes', 'MBI09_g01820_MAGBIO' => 'mbi', 'MBI09_g02146_MAGBIO' => 'mbi', 'MBI09_g40718_MAGBIO' => 'mbi', 'MBI19_g05147_MAGBIO' => 'mbi', 'MBI19_g19941_MAGBIO' => 'mbi', 'MBI19_g19942_MAGBIO' => 'mbi', 'MBI19_g26312_MAGBIO' => 'mbi', 'MBI19_g26316_MAGBIO' => 'mbi', 'MD03G1248700' => 'mdo', 'MD03G1249600' => 'mdo', 'MD03G1249700' => 'mdo', 'MD03G1250000' => 'mdo', 'MD13G1149700' => 'mdo', 'MD13G1149800' => 'mdo', 'MD13G1150200' => 'mdo', 'MD13G1150300' => 'mdo', 'MD13G1150400' => 'mdo', 'MD16G1150000' => 'mdo', 'MD16G1150100' => 'mdo', 'MD16G1150200' => 'mdo', 'MD16G1150600' => 'mdo', 'Medtr2g033630' => 'mtr', 'Medtr4g007280' => 'mtr', 'Medtr4g122660' => 'mtr', 'Medtr4g122712' => 'mtr', 'Medtr4g122718' => 'mtr', 'Medtr4g122720' => 'mtr', 'Medtr4g122740' => 'mtr', 'Medtr4g122750' => 'mtr', 'Medtr4g122760' => 'mtr', 'Medtr4g122780' => 'mtr', 'Medtr4g122800' => 'mtr', 'Medtr4g122890' => 'mtr', 'Migut.M01936' => 'egut', 'Migut.N00030' => 'egut', 'Migut.N00031' => 'egut', 'MSTRG.16314' => 'ama', 'MSTRG.24828' => 'ama', 'MSTRG.24829' => 'ama', 'Nitab4.5_0000651g0280' => 'nta', 'Nitab4.5_0002119g0010' => 'nta', 'Nitab4.5_0002150g0010' => 'nta', 'Nitab4.5_0002150g0080' => 'nta', 'Nitab4.5_0002294g0130' => 'nta', 'Nitab4.5_0004165g0070' => 'nta', 'Nitab4.5_0004809g0010' => 'nta', 'Oeu016575.1' => 'oeu', 'Oeu027346.1' => 'oeu', 'Peaxi162Scf00228g00064' => 'pax', 'Peaxi162Scf00364g00014' => 'pax', 'Peaxi162Scf00548g00645' => 'pax', 'Peaxi162Scf01160g00112' => 'pax', 'Peaxi162Scf01160g00142' => 'pax', 'PGR004G0682' => 'pgr', 'PGR004G1767' => 'pgr', 'PGR004G2339' => 'pgr', 'PGR031G1824' => 'pgr', 'PGR031G2148' => 'pgr', 'PGR031G2424' => 'pgr', 'PGSC0003DMG400004616' => 'stu', 'PGSC0003DMG400004617' => 'stu', 'PGSC0003DMG400004618' => 'stu', 'Phvul.003G116500' => 'pvu', 'Phvul.003G116900' => 'pvu', 'Phvul.003G117100' => 'pvu', 'Phvul.003G117200' => 'pvu', 'Phvul.003G117300' => 'pvu', 'Phvul.003G117400' => 'pvu', 'Phvul.006G119800' => 'pvu', 'Potri.001G288500' => 'ptr', 'Potri.008G102600' => 'ptr', 'Potri.009G083500' => 'ptr', 'Potri.010G063000' => 'ptr', 'Prupe.1G113800' => 'ppe', 'Prupe.1G114500' => 'ppe', 'Prupe.3G007700' => 'ppe', 'Prupe.3G008000' => 'ppe', 'Prupe.3G146800' => 'ppe', 'Prupe.5G112600' => 'ppe', 'Psat0s2734g0040' => 'psa', 'Psat0s2818g0040' => 'psa', 'Psat0s2823g0040' => 'psa', 'Psat0s2823g0080' => 'psa', 'Psat0s4829g0040' => 'psa', 'Psat0s740g0040' => 'psa', 'Psat0s740g0160' => 'psa', 'Psat0s740g0200' => 'psa', 'Psat0s740g0240' => 'psa', 'Psat1g162120' => 'psa', 'Psat4g021360' => 'psa', 'Psat4g021480' => 'psa', 'Psat4g021520' => 'psa', 'Psat4g021720' => 'psa', 'QL06p012819' => 'qlo', 'QL06p012826' => 'qlo', 'QL06p012837' => 'qlo', 'QL06p012845' => 'qlo', 'RcHm_v2.0_Chr2g0143761' => 'rch', 'RcHm_v2.0_Chr2g0144321' => 'rch', 'RcHm_v2.0_Chr3g0482891' => 'rch', 'RcHm_v2.0_Chr4g0399701' => 'rch', 'RcHm_v2.0_Chr4g0425861' => 'rch', 'RcHm_v2.0_Chr4g0425961' => 'rch', 'RcHm_v2.0_Chr4g0426481' => 'rch', 'RcHm_v2.0_Chr4g0432391' => 'rch', 'RcHm_v2.0_Chr4g0432401' => 'rch', 'RcHm_v2.0_Chr7g0200071' => 'rch', 'Rhsim01G0111900' => 'rsi', 'Rhsim03G0038200' => 'rsi', 'Rhsim03G0038300' => 'rsi', 'Rhsim03G0038400' => 'rsi', 'Rhsim03G0038700' => 'rsi', 'Rhsim04G0241200' => 'rsi', 'Rhsim04G0241400' => 'rsi', 'Rhsim05G0218600' => 'rsi', 'Rhsim13G0002900' => 'rsi', 'Sabra08G0077400' => 'sbr', 'Sabra08G0077500' => 'sbr', 'Sabra10G0043600' => 'sbr', 'Sabra10G0043700' => 'sbr', 'SalBow5G1261' => 'sbo', 'SalBow8G1966' => 'sbo', 'SalBow8G3310' => 'sbo', 'Sc12g0010290' => 'sci', 'SGA_v2.0_scaffold246G44798' => 'sas', 'Solyc12g099190.1' => 'sly', 'Solyc12g099200.2' => 'sly', 'Solyc12g099210.2' => 'sly', 'Sopen12g033870' => 'spe', 'Sopen12g033880' => 'spe', 'Sopen12g033890' => 'spe', 'Sp3g15350' => 'spa', 'TAR365G0500' => 'tar', 'TAR365G0682' => 'tar', 'TAR365G1026' => 'tar', 'THA.LOC104820315' => 'tha', 'THA.LOC104820316' => 'tha', 'Thecc.01G317500' => 'tca', 'Thecc.04G304700' => 'tca', 'Thecc.04G304900' => 'tca', 'Thecc.04G305000' => 'tca', 'Thhalv10011825m.g' => 'esa', 'Thhalv10021610m.g' => 'esa', 'Thhalv10021672m.g' => 'esa', 'TPR.G20932' => 'tpr', 'TPR.G25390' => 'tpr', 'TPR.G25397' => 'tpr', 'TPR.G25399' => 'tpr', 'TPR.G25400' => 'tpr', 'TPR.G25401' => 'tpr', 'TPR.G25407' => 'tpr', 'TPR.G25409' => 'tpr', 'TPR.G25429' => 'tpr', 'TPR.G33864' => 'tpr', 'TWI09G1118' => 'twi', 'TWI12G1112' => 'twi', 'TWI53G0804' => 'twi', 'TWI75G0074' => 'twi', 'unitig_748.g7375' => 'ugi', 'VMungo0540G0744' => 'vmu', 'VMungo1215G0431' => 'vmu', 'VMungo1215G0592' => 'vmu', 'VMungo1215G1199' => 'vmu' ) $gf_id = 'HOM05D001578' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001578' ) $data_identifier = 'HOM05D001578' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 3, 'ath' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 10, 'cansat' => (int) 2, 'chi' => (int) 7, 'cru' => (int) 3, 'car' => (int) 6, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 7, 'cil' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 15, 'fve' => (int) 12, 'gma' => (int) 13, 'ghi' => (int) 10, 'gra' => (int) 5, 'han' => (int) 7, 'cav' => (int) 6, 'hma' => (int) 2, 'lal' => (int) 17, 'lja' => (int) 7, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 6, 'mbi' => (int) 8, 'mdo' => (int) 13, 'mtr' => (int) 12, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 7, 'oeu' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 3, 'pvu' => (int) 7, 'ptr' => (int) 4, 'ppe' => (int) 6, 'psa' => (int) 14, 'qlo' => (int) 4, 'rch' => (int) 10, 'rsi' => (int) 9, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 1, 'sas' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 3, 'tha' => (int) 2, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 4, 'ugi' => (int) 1, 'vmu' => (int) 4 ) $gf_gene_species = 'vmu' $gf_gene_id = 'VMungo1215G1199' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 0